Depth and time-dependent heterogeneity of microglia in mouse hippocampal slice cultures

• Microglia exhibit layer-specific morphological properties in slice cultures.
• Microglia exhibit a layer-specific activation state in slice cultures.
• The density of resting microglia changes with culture time.

Microglia are the brain-resident immune cells with the phagocytic capacity to engulf dead and living neurons in health and disease. However, the mechanisms underlying the neuron-microglia interaction remain elusive partly because proper in vitro systems are lacking. Specifically, the highly activated status of microglia with amoeboid morphology in primary culture is different from the ‘resting’ microglia with multiple processes in vivo. Here, we performed a detailed investigation of microglial properties in mouse hippocampal slice cultures, focusing on the changes in morphology in the activated state, finding a depth and time-dependent localization of in vivo-like microglia in slice cultures.